Shinobi of the Clone Wars
by Darkmagicdragon
Summary: A dark and powerful disturbance in the Force has made itself known to a certain few throughout the galaxy. None know what could cause such a great disturbance. Only that it could only bring about a maelstrom of destruction in the galaxy. However, could it also bring about peace? Only time will tell as Naruto Uzumaki travels down a long and winding road.


**Disclaimer; I don't own either Naruto or Star Wars: The Clone Wars. They both belong to their respective creators.**

**Hello to everyone reading this right now. I know it's been awhile. Okay! A few years since I last wrote or updated anything. I'm sorry for that, truly I am. I wanted to graduate from high school since this stuff was cutting in on my grades a little bit. No worries though, because I'm back!**

**Now, let me start off by saying that this is a remake of my old crossover with Naruto and Star Wars: The Clone Wars. I apologize for those of you who loved it, but I'm afraid that I will discontinue Jedi or Sith in favor of this new story.**

**Now before you read, I want to address some things that have changed in this.**

**1) Naruto will be a Sith for a longer period of time, up until season 2.**

**2) Naruto will be more darker than he was in the previous story, but he's not entirely evil. He will have a few people in the beginning that make him less dark, but when on the battlefield he is like an entirely different person. **

**3) Naruto's harem will be kept at a minimum of _seven _girls and only _seven_! I can't stress that enough! This is who they are. Hinata Hyūga, Ahsoka Tano, Aayla Secura, Riyo Chuchi, Shaak Ti, Barriss Offee, and Oola. That's the harem, so please don't ask me to add anyone else! **

**4) The chapters will take place according to the timeline. This means that the episodes of Star Wars: The Clone Wars will come out in chronological order as based on the timeline. I'm not sure if anyone knew this, but the order in which battles took place did not happen that way. Just like how the Star Wars movies first came out in theaters. **

"Normal Speech"

_'Thought Speech' _

**"Demonic Speech"**

_"Hologram / Comlink Speech" _

**Now that this has all been established, how's about we start the story?!**

* * *

_"The shroud of the dark side has fallen. Begun, the Clone War has." _

_—Yoda_

* * *

**Chapter 1: A New Force**

**The galaxy is a vast and wondrous place full of mystery. **

**Many have traveled the stars of the galaxy for eons. **

**Yet there are still many new discoveries to be made. **

**One of these discoveries will shape the very destiny of the galaxy. **

**This is the story of a hero. **

**A hero once lost in the dark, but found his way using other people's light.**

**(Serenno – Dooku's Palace)**

Within a castle on the planet Serenno, the former Jedi Master turned Sith Darth Tyranus, more well known as Count Dooku, is seen inside his office checking over multiple forms regarding all of his speeches and rallies. Recently, the old man has been busy after starting what many have been calling the Separatist Crisis, which has started with the secession of several star systems from the Galactic Republic to form the Confederacy of Independent Systems.

So far, everything that's happened has been going according to his plan, which was to form the CIS with the combined forces of the Trade Federation, InterGalactic Banking Clan, and Techno Union in order to pool their droid armies to overwhelm the Republic.

Just as Dooku had finished going over his progress, his eyes widened as he felt a great disturbance in the Force. Something out in the galaxy was releasing an unrestrained force of wild and untamed power far greater then anything the former Jedi has ever felt before in his life.

_'What is this immense power? It's unbelievably more powerful then either Lord Sidious or myself. What could possibly hold such vast power?' _Dooku thought, wondering what creature could possibly possessed such power.

**(Coruscant – Jedi Temple)**

Count Dooku wasn't the only one to feel this mysterious disturbance in the Force. Within the Jedi Temple, Jedi Grand Master Yoda sat in his private quarters meditating before he senses a great disturbance in the Force. This caused the short green Jedi to suddenly open his eyes in shock at feeling something so powerful.

"A great disturbance in the Force, I sense. Revealed itself, something very strong with the Force has. Very powerful, yet uncontrolled. Send someone to investigate this, we must." Yoda said before standing up from his meditation pad and headed to the door.

**(Serenno – Dooku's Palace)**

Just as Dooku was composing himself, he looks to his desk and finds an incoming communication from his master. Dooku immediately answers the communication before kneeling down just as a hologram of a hooded figure of Darth Sidious appears before him.

"Greetings, my master." Dooku greeted.

_"Lord Tyranus, I have felt a great disturbance in the Force. Something powerful has revealed itself. I trust you sense it as well, my apprentice?"_ Sidious asked, to which Dooku nodded.

"Indeed I have, my master. Whatever it may be, it's power is quite vast. Stronger then any Force-sensitive of our time." Dooku stated.

_"Yes it is. Quite powerful indeed. Which is why if we can find and use whatever entity holds such a power, we could have a Sith powerful enough to destroy the Jedi once and for all."_ Sidious said darkly.

"I see. A Force-sensitive powerful enough to match even young Skywalker. Very interesting, but where might I we find this powerful Force-sensitive?" Dooku asked, to which his master pulled out a holoprojector and activated it to reveal hologram of a world Dooku didn't recognize.

_"This world is where I sense this mysterious entities power coming from. It's an uncharted planet in the Outer Rim of the Unknown Regions. I have already sent you the coordinates. I want you to go to this world, find this entity, and train them as your apprentice."_ Sidious ordered, receiving a nod from Dooku.

"It will be done, my master." Dooku stated, just before the hologram faded away and the Sith Lord stood up to do as his master ordered.

He quickly made his way outside his palace, boarded his solar sailer, and upon flying into to space, entered hyperspace towards the unknown world.

**(Earth – The Final Valley)**

Dooku's ship later exited hyperspace over Earth before flying towards the world and landing in a forested area to hide his ship from view. He exited the ship and quickly made his way toward the place he sensed the disturbance in the Force and came upon a rather impressive sight, a massive valley filled with a deep lake, a waterfall running down from the cliffs above, and two massive statues on both sides of the waterfall of two individuals. However, what caught Dooku's main focus was the destruction around the valley.

_'Such destruction. Whatever caused this must be more powerful then I believed.'_ Dooku thought before spotting two young men down below near the edge of the lake.

One was a black haired boy standing above the unconscious body of a blond boy with whisker marks. Dooku watched as the boy standing over the other stares down at the blond with no emotion to his face as it begins to rain, to which Dooku raising his hood over his head to keep dry. He observes as the looks to be wracked with pain as he falls to the group, still staring at the blond before rising up to his feet and leaving the area.

As Dooku waited until the black haired boy had completely left before making his down to the unconscious blond. Upon getting closer to the boy, Dooku could sense that he was the one to cause the disturbance in the Force with a dark power that the former Jedi is completely unfamiliar with.

"So, this is the one with such a powerful connection to the Force. This is most impressive, especially for someone so young and with untapped potential. With time, he will make a fine Sith." Dooku stated, but before he could grab the blond, a blade appeared in front of his neck.

"Just who the hell are you and what are you trying to do with Naruto?" A silver haired man asked as he pressed his blade closer to the Sith Lord's throat.

"Who I am is of no concern to the likes of you and what I have in store for the boy even more so. What you should be aware of however, is that you are dealing with a Sith." Dooku stated before grabbing and activating his lightsaber.

He slashed at the man, who jumped back just in time to avoid being cut in half, but before he could react, Dooku quickly raised his empty hand at him and shot a wave of Force lightning that electrocuted the man while also pushing him back before the attack ended with the man panting hard, but still standing.

"Interesting. You're much stronger then you appear. However, I'm afraid that I haven't the time to deal with you right now. If you leave now, you won't be harmed. If you stay, you'll die." Dooku warned.

"I don't care. You're not taking Naruto without a fight." The man said, readying to attack again.

"So be it then." Dooku said before shooting Force lightning the man again, who quickly dodged as he ran at Dooku. "You're very skilled, but not skilled enough to face me."

Dooku dodged to the side to avoid being stabbed, he leaned back to avoid a slash, and finding an opening slashed his lightsaber at the man, cutting him across his torso and causing the man to yell out in pain.

Dooku quickly followed up by raising his hand and shooting Force lightning at the man, causing him to cry out in agony before Dooku finished him off by Force pushing him into the cliff side very hard, greatly dazing the man as he fell to the ground unable to move.

Satisfied with his work, Dooku turned and grabbed the now identified Naruto and heaved him onto his shoulder before heading for his ship. As Dooku walked away, the downed man reached out towards his retreating form, desperately trying to get Naruto back.

"N-No. N-Naruto." The man said in vein before passing out from the pain.

Dooku ignored the man's plea as he jumped up the cliff side and headed for his ship. After boarding his solar sailor and making sure the boy was secure, Dooku ordered his droid pilot to leave the world and return to Serenno.

**(Serenno – Dooku's Palace)**

Upon returning to Serenno, Dooku immediately had a medical droid take Naruto to the medical center and place him in a bacta tank to heal. With some time on his hands, Dooku could only wait until the medical droid informed him of the blonds condition. Until then, he decided to contact his master to inform him of his success in finding the boy.

_"Report, Lord Tyranus. Were you successful in finding what was causing the disturbance in the Force?"_ Darth Sidious asked.

"Indeed I was, Lord Sidious. As it turns out, the disturbance in the Force was caused by a boy who possesses a great power within him. Power far more different then that of the Force." Dooku informed.

_"I see. This is most unprecedented, but quite interesting to learn."_ Sidious said to himself before looking to Dooku. _"Have you taken a blood sample to find out what his midi-chlorian count is?" _

"I have, my master. As it turns out, the boy has a midi-chlorian count over 20,000. The same as young Skywalker's." Dooku answered, surprising Sidious.

_"A second person with such a high midi-chlorian count is unheard of. This is very unexpected."_ Sidious stated, thinking hard on the matter before smirking. _"If this is true, then we could have a second Chosen One in our midst. One to match the Chosen One of the Jedi. If we train the boy in the ways of the dark side of the Force, he could become a Sith powerful enough to destroy the Jedi, including Skywalker."_

"I believe you are correct Lord Sidious, but I feel as though it may harder then you expect. The boy is quite powerful, so teaching him loyalty shall be difficult." Dooku stated, but Sidious had an idea.

_"You are right, the boy is most powerful indeed and no doubt will not stay loyal to us so easily. That is why I have an idea to ensure his obedience. You will use the Force to search the boy's mind and learn everything you can about him. Once you do, use what you learn to fool the boy into joining us."_ Sidious said, receiving a nod from Dooku.

"It will be done, my master." Dooku stated.

_"Good. Once that is done and you receive his loyalty, I wish for you to train him to be a Sith. It may go against the rule of two, but it will be worth it to have such a power in our control instead of the Republic."_ Sidious stated, receiving an agreeing nod from Dooku before his hologram faded away.

None too soon, the medical droid entered Dooku's office.

"Sir, the boy is fully healed, but is still unconscious. If you wish to see him, you may." The droid stated.

"Very good. I'll go check on him then." Dooku said as he followed the medical droid to the medical center of his palace.

Upon entering the medical center, Dooku found Naruto still unconscious just as the droid had said while laying on an examination table.

"Perfect. This gives me the perfect opportunity to learn just who you are boy and find out how to turn you to the dark side." Dooku stated before placing his hand on Naruto's head and using the Force to learn everything that his memories have to hold.

**(Dooku's Palace – Medical Center)**

Upon doing this, Dooku learned that the boy's name is Naruto Uzumaki, Shinobi of Konohagakure from the planet Earth. He also learned all of the things that Naruto loves, hates, fears. Even the Kyuubi. After learning of the blond's fears, Dooku decided to use them to bring the boy to the dark side. Though he felt there were more memories, something was preventing him from doing so. Whatever it was, Dooku couldn't use the Force to bypass it. The Sith Lord suspected it was this Kyuubi sealed inside the boy that was the cause of it.

_'Even so, it matters not. I've learned quite enough to turn him to the dark side.'_ Dooku thought before watching the boy slowly wake up.

Naruto groaned as he awoke. As he sat up and rubbed his head, he refreshed his memory to recall what happened in his fight with Sasuke. The last thing he remembers was Sasuke and him inside of a sphere of chakra created by their Rasengan and Chidori colliding.

"Oh man. What happened? The last thing I remember is Sasuke and me jumping at each other with our Rasengan and Chidori colliding and creating a ball of energy that pulled us inside. The last thing I saw was Sasuke staring back at me before everything went black." Naruto said before his eyes opened to show their blue color. "Did I do it? Did I beat Sasuke and bring him back home?"

"I'm afraid not." An unknown voice answered.

Naruto looked up and found an old man looking at him. He didn't know who he was, but Naruto kept his guard up in case he was an enemy. He tensed when the man raised his hand.

"Calm yourself young man, I'm not going to hurt you. Quite the opposite really. I'm the one who saved you from death." Dooku said, calming Naruto just a little.

"Who are you? Where did you take me? And what do you mean by saved me?" Naruto asked.

"My apologies. My name is Count Dooku and I've brought you to me palace on the planet Serenno." Dooku said, letting the first two things sink in to the now surprised blond.

"W-Wait. Hold on a second. What do you mean planet Serenno? Are you saying we're on another planet with life?" Naruto asked, getting a nod from Dooku. "B-But how? I thought only Earth had life on it."

"Young man, you have much to learn. The galaxy is far more vast then you know of. Filled with countless worlds you've never heard of, many creatures you've never seen before, and technology you could have never imagined." Dooku stated, much to Naruto's growing surprise.

"B-But why am I here? If what you're saying is true, then I want you to take me back to Earth right now! I have to save Sasuke! I need to get back to my friends! They all need me, so take me home right now old man!" Naruto yelled.

"Why would you want to go back home when one of your comrades tried to kill you while you were unconscious?" Dooku questioned, making Naruto look at him in skepticism.

"What are you talking about? None of my comrades would try to kill me. You're lying!" Naruto accused, making Dooku mentally smirk at the blond walking into his trap.

"Oh? Is that what you believe? Because when I found you, I saw a masked, silver haired man leaning over you with a kunai at your throat ready to kill you." Dooku said, making Naruto look at him in shock.

"What? No. Y-You can't be talking about Kakashi-sensei. He'd never try to kill me." Naruto said disbelievingly.

"Oh, but he did." Dooku said, before continuing. "I stepped in and prevented him from killing you and when asked why he tried to do it, he said that it was because he was ordered by the Hokage to search for the Nine-Tails Jinchuuriki while he and his comrades were on their mission and kill him to protect the village."

Naruto could only stare at the old Sith in shock, not believing what he was hearing. He didn't know what to think. He could only listen as the man continued.

"He said that it was a side mission of your comrades, which was to kill you and make it appear as though you were killed in the line of duty in bringing your friend back. However, they failed due to interference. So, it fell into Kakashi's hands to kill you himself. Something he said that he's wanted to do the day he saw you." Dooku explained, watching as Naruto took in all that he's said with absolute disbelief.

"N-No. Th-That can't be… it just…." Naruto stammered out, not knowing what to say. "How?"

Dooku was going to ask him how what, but was stopped when Naruto slammed his fist into the table, denting it.

"How the hell can they do this to me?! After all that I've done for them and this is how they repay me?!" Naruto yelled, his eyes turning red with slitted black pupils. "All of my hard work to protect my village! The people I thought were my friends! My dream to become the Hokage! All of it was absolutely pointless!"

_'Perfect. Just as planned.'_ Dooku thought before continuing on with his lies. "I understand your pain boy. It's quite upsetting when the people close to you turn their backs on you and betray you."

Dooku watched as the boy calmed down, but soon broke down in front him and covered his face in his hands, trying his hardest not to cry.

"What am I going to do now? Where will I go? How will I live? I don't know what to do. I'm lost without my friends and my home. I don't have anything to live for anymore. I'm alone and powerless." Naruto questioned himself, having no idea what to do now that he's lost everything.

"It hurts, doesn't it? All the pain they've caused you. They made you believe they were your friends, but actually hated you. You became strong to protect what was precious to you and they spit on all that effort. Everything they've done for you was an illusion, because in the end they betrayed you're trust and loyalty." Dooku stated, making Naruto angry as he remembered all the times he's been with his so called friends. "Don't you feel as though they deserve to feel the same pain that they put you through? To make them suffer for betraying you?"

"Y-Yes. Yes I do, but I don't have the power to do it by myself. I want to get stronger. No. I need to get stronger. I need more power then I have now. The Kyuubi is powerful, but I refuse to use it. I want the power to make them all suffer one by one with my own hands before I finish them off." Naruto said, his anger speaking over his rational sense of mind.

"Not to worry, because I can give you that power. I can train you to use the dark side of the Force. With it, you can do whatever you please and more. All that I ask for in return is your absolute loyalty. What do you say?" Dooku asked, already knowing the answer.

Naruto said nothing for a moment before lowering his head to shadow his eyes and speaking.

"I will do whatever you ask." Naruto stated, getting a smirk from Dooku.

"Very good, my apprentice." Dooku said darkly.

**(Three Years Later – Unknown Location) **

Three years have passed since that fateful day when Naruto Uzumaki became the apprentice to the Sith Lord Count Dooku. Since that day, Dooku has trained Naruto in the ways of the dark side of the Force. To start off his training, the Sith Lord taught Naruto to harness the Force around him. Improve his martial prowess. Even construct and use his own pair of lightsabers. Whilst doing this, Naruto trained with his ninjutsu and taijutsu so as to make himself a deadly adversary for whoever he fights.

The training in which he was put through later after that was the most brutal thing Naruto has ever experienced before in his life. He trained until he collapsed from exhaustion only to get back up and keep going. He was tortured mentally and physically to the point of almost being driven insane. Even forced to fight for his very survival against hundreds of assassin droids and wild beasts on a remote world for an entire month. All of this would have killed a weaker man, but Naruto survived it all and came out on top.

Said blond is currently sitting on the ground meditating in the center of a circular room with bright white lights and a single door being the only way in or out. After three years of being Dooku's apprentice, Naruto's appearance has drastically changed as a means of showing off his choice in becoming a Sith.

Naruto now wears a sleeveless, orange trimmed, hooded black jacket, often left open, a black half mask connected to a sleeveless black shirt and matching black pants, complete with a waist-guard, fingerless opera-length black gloves, an orange trimmed, black waist cape that reaches his knees, held by a black leather belt with a square-shaped buckle, and black shinobi boots. On his belt are two black and grey, cylindrical lightsaber hilts with claw-like emitters.

Right now, Naruto is currently waiting for his upcoming test. He didn't have to wait long, because the lights in the room shut off, shrouding the room in total darkness. Naruto didn't even react when the door opened and he heard multiple metallic footsteps enter the room walking around him until he knew that he was surrounded and the door soon shut again. Now that his test has arrived, Naruto slowly stood up with his eyes still closed. The moment he was on his feet, the sound of electrostaffs activating caught his attention.

_'MagnaGuards? This should be interesting.'_ Naruto thought to himself, ready for action.

One of the MagnaGuards behind Naruto ran at him first with its electrostaff raised above its head in an attempt to strike down the seemingly unsuspecting blond. However, it didn't get the chance before Naruto's eyes snapped open while grabbing his right lightsaber, activating its crimson blade, and cutting the droid down with a single slash to the torso.

The other droids in the room stared down at their fallen brother before looking back up at the blond, who raised his empty hand and gave them the "come here" motion.

"Bring it." Naruto said simply.

That was all the MagnaGuards needed to hear before they all ran at the blond. Naruto weaved his way around or defended against the droids attacks as they swung at him from every direction. Just as one MagnaGuard thought it was about to land a hit on the blond's face, Naruto moved his head and let the electrified end of the staff pass by without flinching. Before the droid could pull its weapon back, Naruto cut its arms off. He finished the disarmed droid by raising his lightsaber and cutting it down the middle, destroying it.

Two MagnaGuards tried to attack the blond from above and below, but the blond jumped over the bottom attack and ducked under the overhead attack. Before they knew what happened, Naruto cut their heads off and Force pushed them into the walls, crushing their bodies in the process. Naruto smirked under his mask before turning to the six remaining MagnaGuards.

"Four down, six to go. Who's next?" Naruto asked in amusement.

Two MagnaGuards cautiously walked towards Naruto before attacking with offensive thrusts and protecting themselves with defensive spins of their electrostaffs. This forced Naruto to block their strikes before doing the same, only to be blocked himself. As this was happening, he took into account that the other four MagnaGuards were blocking his sides to prevent him from getting around them while they look for an opening to attack him.

With that, Naruto Force pushed them all away from him to give himself some room. He grabbed his second lightsaber and ignited it while wielding it in a reverse grip. Naruto ran at three MagnaGuards and cut one to pieces before it could defend itself. One tried to strike him from behind, but was blocked by Naruto raising his lightsabers over his head before Naruto spun around and delivered a powerful kick to its face, sending the droid flying into its comrade. Before Naruto could destroy them, he jumped back to avoid having his face hit.

A MagnaGuard thrust his electrostaff at the blond, only for him to block it with one lightsaber and cut off the droid's arm and both legs with his other. Before the droid could hit the ground, Naruto caught it with the Force and Force pushed it into one of the MagnaGuards that ran at him with enough power to send it into the wall, getting crushed as a result. After seeing this, the last three MagnaGuards prepared themselves for anything to come.

"As fun as this was, I'm afraid I'm done with you guys." Naruto stated while deactivating his lightsabers and placing them on his belt.

This caused the MagnaGuards to look at the blond in what could only be confusion as he placed his hand on one of his gloves and, in a puff of smoke, pulled a kunai out of thin air. The droids could do nothing as Naruto threw the kunai faster then they could react and stab the middle MagnaGuard in the chest. All three of them looked at it, expecting something to happen, but nothing did. Ignoring it, they were about to approach the blond, only for a sizzling sound to make them look at the kunai again that was somehow sparking.

~BOOM!~

"Should've taken it out when you had the chance trash can. Oh well. Too late now." Naruto said as he walked to the last MagnaGuard that survived the explosion with its limbs damaged and cut its head off.

The moment Naruto finished off the droid, the lights turned back on and the door opened, revealing Dooku. Upon seeing his master, Naruto deactivated his blades and placed on his belt before kneeling before the old man.

"Master." Naruto greeted.

"Well done, Naruto. Most impressive." Dooku congratulated as he took in the destroyed droids in the room. "Your skills have greatly improved far beyond what they once were in the beginning."

"Thank you, my master." Naruto said, grateful for the rare complement.

"This is good, because your skills will soon be required." Dooku said, making Naruto look up at him in curiosity.

"Why is that?" Naruto asked.

"The Clone War has begun." Dooku answered.

This news made Naruto smirk under his mask in excitement knowing that he will soon make his presence known to the Republic and the Jedi Order.

"Finally."

**To Be Continued… **

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**Okay people, that was chapter one of my Naruto x Star Wars: The Clone Wars rewrite. I do who you like it and can I just say it's good to be back. Sorry for being away for awhile, but I had to focus on other matters for some time regarding my grades. It's not that my writing cut into my work, just that I didn't have much time for it because I was exhausted from being in school eight hours a day. Anyway, I'm back and will try to get back on track with my writing.**

**Now, I know some of the questions you guys will ask. Will Naruto destroy Konoha? Will Naruto know Force lightning? What are Naruto's lightsabers? Is Naruto going to be a Gray Jedi? Can Naruto have other girls in his harem? What kind of ship does he have? Etc. etc.**

**People, these are questions meant to be answered as you read. If you want to know, then keep reading. However, I will be generous and answer two of these questions right off the bat. These are Naruto's lightsabers and his ship. Naruto's lightsabers are the Sith Stalker's from the Force Unleashed and his ship is the one that belonged to Darth Maul. **

**[Naruto's Lightsaber]**

**-Production Information-**

Model: Paired lightsabers

Type: Single blade

Creator: Naruto Uzumaki

Date Created: Before the Clone Wars

Owner: Naruto Uzumaki

**-Physical and Technical Specifications-**

Hilt material: Alloy metal

Crystal: Kyber crystal

Blade color: Red

Blade length: Average

Design: Cylindrical hilt with a claw emitter

**[Sith Infiltrator – The _Kyuubi's Wrath_]**

**-Production information- **

Manufacturer: Republic Sienar Systems

Model: Heavily modified Star Courier

Class: Armed star courier

**-Technical specifications- **

Length: 26.5 meters

Maximum speed (atmosphere): 1,180 kph

Countermeasures: Cloaking device

Armament: Concealed laser cannons (6), Proton torpedo launcher


End file.
